Identificaiton of the dITP- and XTP-Hydrolyzing Protein from Escherichia coli

Chung, Ji Hyung; Park, Hyun-Young; Lee, Jong Ho; Jang, Yangsoo

doi:10.5483/bmbrep.2002.35.4.403

Cited by 21 publications

(21 citation statements)

References 31 publications

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“…However, loss of the similar YjjX nucleoside triphosphatase, even in combination with loss of RdgB, had no effect on xanthine or hypoxanthine levels (Table 1). Both enzymes have in vitro activities against (d)XTP and (d)ITP (27)(28)(29), so the results suggest that RdgB is the major xanthine and hypoxanthine nucleoside triphosphatase in E. coli and that the in vivo substrate specificities need to be reconsidered. Finally, the loss of either the nfi gene encoding the EndoV DNA repair protein or the alkA gene encoding the AlkA DNA glycosylase did not affect the levels of xanthine or hypoxanthine in DNA or RNA; the implications of this observation will be discussed shortly in the context of DNA repair.…”

Section: Defects In Purine Nucleotide Metabolism Increase the Levels Ofmentioning

confidence: 99%

“…Misinsertion of damaged nucleotides is partially controlled by polymerase substrate specificity, but a variety of enzymes have evolved to remove noncanonical nucleoside triphosphates from the nucleotide pool. E. coli possesses two nucleoside-triphosphatases, YjjX and RdgB, that cleave (d)XTP and (d)ITP to diphosphate (YjjX) and monophosphate (RdgB) forms (27)(28)(29), which parallels E. coli MutT pyrophosphorylase activity that acts on 8-oxo-dGTP (30). RdgB homologs in S. cerevisiae, mice, and humans (ITPA) possess similar activities (29,31).…”

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Defects in purine nucleotide metabolism lead to substantial incorporation of xanthine and hypoxanthine into DNA and RNA

Pang

McFaline

Burgis

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

111

110

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Deamination of nucleobases in DNA and RNA results in the formation of xanthine (X), hypoxanthine (I), oxanine, and uracil, all of which are miscoding and mutagenic in DNA and can interfere with RNA editing and function. Among many forms of nucleic acid damage, deamination arises from several unrelated mechanisms, including hydrolysis, nitrosative chemistry, and deaminase enzymes. Here we present a fourth mechanism contributing to the burden of nucleobase deamination: incorporation of hypoxanthine and xanthine into DNA and RNA caused by defects in purine nucleotide metabolism. Using Escherichia coli and Saccharomyces cerevisiae with defined mutations in purine metabolism in conjunction with analytical methods for quantifying deaminated nucleobases in DNA and RNA, we observed large increases (up to 600-fold) in hypoxanthine in both DNA and RNA in cells unable to convert IMP to XMP or AMP (IMP dehydrogenase, guaB; adenylosuccinate synthetase, purA, and ADE12), and unable to remove dITP/ITP and dXTP/XTP from the nucleotide pool (dITP/XTP pyrophosphohydrolase, rdgB and HAM1). Conversely, modest changes in xanthine levels were observed in RNA (but not DNA) from E. coli lacking purA and rdgB and the enzyme converting XMP to GMP (GMP synthetase, guaA). These observations suggest that disturbances in purine metabolism caused by known genetic polymorphisms could increase the burden of mutagenic deaminated nucleobases in DNA and interfere with gene expression and RNA function, a situation possibly exacerbated by the nitrosative stress of concurrent inflammation. The results also suggest a mechanistic basis for the pathophysiology of human inborn errors of purine nucleotide metabolism.DNA and RNA damage | mass spectrometry | nucleobase deamination | purine metabolism | DNA repair T he chemical modification of nucleobases in DNA and RNA can arise from both physiological and adventitious mechanisms at all stages of nucleic acid metabolism. This is particularly true for deaminated versions of the nucleobases. As shown in Fig. 1 for purines, nucleobase deamination in DNA and RNA leads to the formation of 2′-deoxy-and ribonucleoside forms of hypoxanthine (2′-deoxyinosine, dI; inosine, Ino) from adenine, xanthine (2′-deoxyxanthosine, dX; xanthosine, Xao) and oxanine (2′-deoxyoxanosine, dO; oxanosine, Oxo) from guanine, and uracil (2′-deoxyuridine, dU; uridine, Urd) from cytosine (1). All of these products are miscoding and mutagenic in DNA (2-4) and can interfere with RNA editing (5) and the function of noncoding RNAs (6).There are three recognized mechanisms that contribute to nucleobase deamination in DNA and RNA, the simplest of which is hydrolysis (7). A second source of nucleobase deamination is associated with the nitrosative stress caused by increases in nitric oxide-derived nitrous anhydride during inflammation (1). A third mechanism is associated with deaminase enzymes acting on RNA and DNA, with activation-induced cytidine deaminase converting cytidine to uridine during immunoglobulin diversification in B lymphocytes an...

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Section: Defects In Purine Nucleotide Metabolism Increase the Levels Ofmentioning

confidence: 99%

mentioning

confidence: 99%

Defects in purine nucleotide metabolism lead to substantial incorporation of xanthine and hypoxanthine into DNA and RNA

Pang

McFaline

Burgis

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

111

110

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“…Moreover, DNA in rdgB mutants accumulates EndoV-recognized modifications (Bradshaw and Kuzminov 2003). Biochemically, the RdgB protein is an NTPase with a 100-fold preference for the noncanonical nucleotides ITP, XTP, and dITP (Chung et al 2001(Chung et al , 2002. It is likely that RdgB hydrolyzes noncanonical DNA precursors dITP and dXTP to monophosphates, preventing incorporation of the base analogs hypoxanthine and xanthine into the chromosomal DNA (Bradshaw and Kuzminov 2003).…”

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Chromosomal Fragmentation Is the Major Consequence of the rdgB Defect in Escherichia coli

Lukas

Kuzminov

2006

Genetics

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“…For example, dUTP is hydrolyzed to dUMP by deoxyuridine triphosphatase (2, 16), encoded by the dut gene (19). Indirect evidence (5; B. Budke and A. Kuzminov, unpublished data) strongly suggests that dITP and dXTP are the relevant in vivo targets of the RdgB protein, which is characterized in vitro as the dITP-and XTP-pyrophosphatase of E. coli (dXTP has yet to be tested) (7,8).Interception of noncanonical DNA precursors can be an important strategy in preventing mutagenesis due to the presence of a particular base analog in the DNA. For example, while mutM and mutY mutants, deficient in base excision repair of, or opposite to, 8-oxoguanine in DNA, show increased GC3TA transversion mutagenesis (15), mutT mutants, deficient in the interception of the noncanonical DNA precursor 8-oxo-dGTP, show an even stronger transversion mutagenesis in the opposite direction (AT3CG) (15).…”

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Hypoxanthine Incorporation Is Nonmutagenic in Escherichia coli

Budke

Kuzminov

2006

J Bacteriol

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Endonuclease V, encoded by the nfi gene, initiates removal of the base analogs hypoxanthine and xanthine from DNA, acting to prevent mutagenesis from purine base deamination within the DNA. On the other hand, the RdgB nucleotide hydrolase in Escherichia coli is proposed to prevent hypoxanthine and xanthine incorporation into DNA by intercepting the noncanonical DNA precursors dITP and dXTP. Because many base analogs are mutagenic when incorporated into DNA, it is intuitive to think of RdgB as acting to prevent similar mutagenesis from deaminated purines in the DNA precursor pools. To test this idea, we used a set of Claire Cupples' strains to detect changes in spontaneous mutagenesis spectra, as well as in nitrous acid-induced mutagenesis spectra, in wild-type cells and in rdgB single, nfi single, and rdgB nfi double mutants. We found neither a significant increase in spontaneous mutagenesis in rdgB and nfi single mutants or the double mutant nor any changes in nitrous acid-induced mutagenesis for rdgB mutant strains. We conclude that incorporation of deaminated purines into DNA is nonmutagenic.Three of the four DNA bases-cytosine, adenine, and guanine-have amino groups. Deamination of these three bases ( Fig. 1) generates the base analogs uracil, hypoxanthine, and xanthine, which have pairing specificities different from the original bases. Therefore, the cell employs excision repair to prevent mutagenesis due to spontaneous DNA base deamination. For example, in Escherichia coli, uracil-DNA glycosylase encoded by the ung gene initiates excision of uracils from DNA (12, 30). The ung mutants experience a 30-fold increase in GC3AT transitions (13), owing to the deamination of cytosine to uracil in the DNA (31). Deamination of adenine to hypoxanthine in the DNA (24) is also known to cause mutations: hypoxanthine preferentially base pairs with cytosine (3,18,35,39,51), and its formation in DNA, for example, as a result of nitrous acid exposure, leads to AT3GC transitions (45). Hypoxanthine removal from DNA in E. coli is initiated by the product of the nfi gene, endonuclease V (Endo V) (53, 54), and, to a much lesser extent, by the product of the alkA gene, 3-methyladenine-DNA glycosylase (43,44). Although nfi mutants do not show increased spontaneous mutagenesis, they are more mutable by nitrous acid (45), an agent known to promote deamination of DNA bases (55).Bases can deaminate not only in DNA but in nucleotides as well, both chemically (32, 46) and enzymatically (56). Deamination of DNA precursors should lead to accumulation of noncanonical nucleoside triphosphates in the cell's DNA precursor pool. These noncanonical nucleotides, such as dITP, dXTP, and dUTP, can be incorporated into the newly synthesized DNA, albeit less efficiently than regular DNA precursors (3,38,42,51). Noncanonical DNA precursors are actively intercepted and removed from the DNA precursor pool. For example, dUTP is hydrolyzed to dUMP by deoxyuridine triphosphatase (2, 16), encoded by the dut gene (19). Indirect evidence (5; B. Budke and A....

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Identificaiton of the dITP- and XTP-Hydrolyzing Protein from Escherichia coli

Cited by 21 publications

References 31 publications

Defects in purine nucleotide metabolism lead to substantial incorporation of xanthine and hypoxanthine into DNA and RNA

Defects in purine nucleotide metabolism lead to substantial incorporation of xanthine and hypoxanthine into DNA and RNA

Chromosomal Fragmentation Is the Major Consequence of the rdgB Defect in Escherichia coli

Hypoxanthine Incorporation Is Nonmutagenic in Escherichia coli

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